Malinga, who has taken 291 wickets in 191 ODIs with his unique slingshot action, has remained in Sri Lanka to rehab the injury he sustained against the West Indies early last month.
The 32 year-old, who retired from test cricket in 2011, has been replaced in Sri Lanka's squad by all rounder Thisara Perera.
Malinga is the second fast bowling casualty since Sri Lanka started their tour with a warm-up game in Queenstown earlier this month - Dhammika Prasad, the spearhead of the test pace attack, suffered a back injury in that game and returned home.
New Zealand also has a slight concern ahead of the opening game of the five-match series at Christchurch's Hagley Oval on Boxing Day. Premier batsman Kane Williamson is potentially in doubt, also with a knee injury.
The newly-crowned world No 1 test batsman, according to the International Cricket Council, hurt his right knee while fielding in the second test against Sri Lanka in Hamilton.
He was visibly favouring the joint but it did not prevent him guiding the Black Caps to a five-wicket victory at Seddon Park with an unbeaten 108.
Test opener Tom Latham is on standby, hours after being named in Canterbury's Ford Trophy squad to play defending champions Central Districts in the opening round of the domestic one-day competition in Napier on Sunday.
Black Caps batting coach Craig McMillan said Williamson would not be risked given there is a busy schedule ahead.
"We're just working through that knee. It's just a little bit niggly so we want to make sure it's a hundred per cent. If it's not Tom is the man we'll bring in as cover.
"We'll see how he feels (on Christmas Day) and make a decision.
"We need to get it right, if a little bit of a break will help it that's something we'll consider," McMillan added.
Williamson spent time with medical staff as teammates, including debutant-in-waiting Henry Nicholls, started their training session with a football game.
McMillan said regardless of Williamson's medical status Nicholls - a 24-year-old left handed strokemaker - would be a strong contender for the first leg of the Christchurch doubleheader.
"He's certainly in the mix when you look at our line-up," said McMillan, who acknowledged Cantabrian Nicholls' familiarity with Hagley Oval worked in his favour.
"I don't think there's any better place to make your debut than at home. He's played a lot of cricket here. It would probably ease the tension a little bit when you know you're on a ground that you've played well at before."
Meanwhile, McMillan was relieved to learn Malinga, who was also scheduled to captain Sri Lanka in two tour-ending T20 internationals, had not joined the tour party.
"That's a big loss, what a contributor he's been over a number of years for Sri Lanka. He's been their key fast bowler.
"He's a handful. I'm sure they'll miss him, but it gives an opportunity to some other younger guys in the squad," McMillan said, referring to Dushmantha Chameera's development in the test series.
The inexperienced 23-year-old quick, who only played two tests before arriving in New Zealand, claimed 12 wickets to lead the Sri Lankan bowling unit and emerge as a possible long-term fixture in the test side.
"He's got raw pace. Anyone who bowls 145 clicks causes some apprehension at times for batsmen. It's good to see a Sri Lankan fast bowler. Normally they've got guys that aren't quite as quick.
"It's great for them. We knew he was still a young kid still learning his trade but his performances over the two tests were exceptional."
Both teams finalise their preparations on Christmas Day.
(stuff.co.nz)